City of Lost Clary
by Callista O'Brien
Summary: What if Jonathan took Clary instead of Jace in City of Lost Souls? This story follows Jace and looks at what would happen if things were reversed and Clary was taken while he wasn't. Hope you like it:)
1. Chapter 1

**Disclaimer! I'm not Cassandra Claire!**

**Hope you like the story!:)**

One day, six hours, and thirty-seven minutes ago I lost the love of my life. I will do anything it takes to get her back. I don't care what it takes. No matter how many buildings I have to burn to the ground or how many times I have to fight Jonathan to the death I will get her back. Clary deserves better than me, but I swear by the angle that I will drag that monster to the depths of hell if he lays one finger on her.

I pull my knees to my chest and shudder, trying not to think about all the things he could have done to Clary. Why oh why did I have to leave her up on that roof with him? Why didn't I volunteer to stay up there with her? Why couldn't I have just seen that he would wake back up and hurt her? The demon wanted to posses me, Clary wasn't even involved, but now they have her.

Salty rain-drops fall from my eyes and I hastily wipe them away with the back of my hand. I hadn't cried since I was a boy and Valentine broke the neck of my hunting falcon, but ever since I walked up on that roof and saw Clary and Jonathan missing with spattered blood on the ground, I've been worse than a girl after a Nicolas Sparks' movie.

I hold in another sob. Clary would have loved that comparison. I have to find her and the Clave is doing next to nothing. I have been out all day and night along with a few others looking for her but there isn't even any evidence besides the blood on the roof to lead us anywhere. The only reason I'm in my room now and not out looking for her is because Alec and Izzy locked me in here, saying that I needed to rest.

I grip my hands tight together until my fingernails make my palms bleed. I let out a vicious cry before punching a hole straight through my wall and into the next room. This is so maddening! Why should I get to rest when Clary is probably going through hell right now? Why does the universe hate me so?

"Jace?" I hear an alarmed voice peep out from the other room who I punched a hole into. Oh yeah I forgot, Alec lives next door.

"I thought you needed another window," I spit maliciously wondering if Clary has any windows where she is. What if she is locked in a windowless room, like some kind of cage? The thought makes me shudder.

"Jace," Alec says, turning into that parental tone that he always used to use on Izzy and I when we were kids and he declared himself the oldest and therefore, in charge. "You know you're going to half to fix that later."

"What does it matter Alec?" I scream. "Clary's gone and no one is doing shit to find her!" I yell. Alec lets out a huff from the other side of the wall. Isabelle says that I am being difficult, that throwing temper tantrums isn't going to help anything. Then what is, Isabelle? Going on halfhearted search parties throughout the city when they are probably out of the country be now?

Suddenly my door flies open and Alec and Isabelle are running in with worried expressions on their faces. I hate that look. Everyone has been giving it to me since I looked around on that roof and broke to the ground when I saw she wasn't there. The sympathy mixed with worry. Like they feel sorry for me, but they don't want to get to close for fear of how I will lash out.

"Jace, punching holes through the wall isn't going to make them find her any sooner." Isabelle says flatly, she is almost in denial over the whole thing, just like Simon. I have never been close to Clary's mother, but at least she feels the same way I do.

"Then what will?" I shout, my chest rising and falling at a heated rate. I lock with Isabelle's eyes and see no answers. This breaks something inside me. No one even knows what to do to get her back. I press my hands into my face, not caring who sees me cry anymore. "What if it is already too late? What if he has already killed her?" I ask roughly.

Suddenly Isabelle's arms are around me, and I feel Alec sit awkwardly on the edge of my bed.

"You can't think like that," she says. "If Jonathan wanted to kill her, then he would have right then on the roof and left her body for us to see. He took her for a reason Jace," I let myself fall against her, not sure how much comfort her words provide me.

"We are going to find her Jace, I know it." Alec says from his perch on my bed.

"Don't lie to me Alec!" I snap at him. "You don't know that! What if we never find her? What if she lives like a prisoner for the rest of her life just because I wasn't thoughtful enough to stay up on the roof with her that night?"

"Jace this isn't your fault, nobody could have known that this would happen," Isabelle tries to reassure me.

"I should have just stayed." I snap with finality.

"Jace," Alec starts, when I suddenly leap out of bed and start heading for the door.

"I'm going to find her." I say with force, blind determination to find my familiar red-headed love driving me forward.

"Jace!" Both Isabelle and Alec cry as they grab my arms and try to hold me back. I struggle against them but unfortunately with the combination of two against one and me not wanting to hurt them, I can't get past.

"You really think that you are going to find Clary in your pajamas after you haven't slept for days and just battled a Demon?" Alec hisses as he puts his full weight into holding me back.

"You need to rest Jace! You're never going to find her, or be able to fight Jonathan in this condition! You can look for her in the morning, after you get some sleep!" Isabelle commands.

After minutes of me pushing against them, I finally give in and let them throw me onto my bed. My thoughts in a haze as all I can think about is Clary, how she talks, how she walks, that cute little face she makes when I say something that I know will annoy her.

"I brought some of Hodge's famous sleep potion. It should knock you out for a little while," Izzy says.

I glare at her, not wanting to take it. What if something happens while I'm out? What if they find Clary but they can't get her back because their best fighter, me, isn't there? No, I am not taking that. I cross my arms in refusal.

Before I know what is happening Izzy lands a hard kick to my shin. I open my mouth to complain when suddenly Alec is pouring the contents down my mouth. I begin to choke, but the liquid slides down anyway. Isabelle and Alec stand over me looking like they just had to give their child a shot. I sneer at them as my eyes start to drop.

"You needed this Jace," Alec says. "Come find us when you wake up and we'll go out with you." With that the two of them leave my room and I am all drugged up and alone.

I fight off fresh tears as my conscious mind slowly starts to shut down and Clary comes back to mind. I'm sorry Clary. I'm sorry that I ever let this happen to you.

My eyelids feel like lead as they crash down, my breathing starting to turn even no matter how much I try to fight it. I am seconds away from being taken by dreams when suddenly an unforgettable, lovable, and complimented by red hair, voice rings through the room.

"Jace?"

**Yay! I hoped you liked it! Please don't be a silent reader and let me know what you thought! I hope to update soon but it all depends on your feedback!:) **


	2. Chapter 2

**Disclaimer! I am not Cassandra Claire!**

**Thank you so much for all of the amazing feedback!:) I'm glad that you're liking it! The next chapter is rather short but I wanted to give you guys something for being so awesome!:)**

My eyes snap open and I sit straight up only to see the best sight in the world. My Clary.

She stands a little ways away from me, looking almost hesitant. So many questions pop into my mind, especially when I see her eyes. The color and shape are both the same, but I fell in love with her for the fire in her eyes, and now that fire is gone.

I leap up and rush over to her, fighting off the sleep potion and throw my arms around her. "Clary? What is going on? Where have you been?" I ask, the questions pouring out of my mouth.

"You have to come with us, Jace," Clary says, sounding exactly the same, but the words don't sound natural coming out of her mouth.

"Us? Who is the us?" I ask. Suddenly Jonathan materializes out of a dark corner.

"With her and I, dear Jace," he answers, a burning hate for him filling my veins as I see him. I start toward him when suddenly Clary throws out an arm, stopping me.

"What are you doing?" I ask her when suddenly the glazed look disappears from her eyes and it looks like se is giving me a warning. Before I have time to figure out what just happened her plain calm face is back on.

"You can't hurt him Jace, we are tied together." She says. I stare at her hard, what does that mean? "He has big plans that you can be a part of if you just listen," Clary says in that same robotic voice that she has been using since she first came here.

"What do you mean tied together?" I snap, starting to get fed up with all this weirdness and just wanting to hold Clary in my arms. Suddenly a muffled voice comes from next door.

"Jace?" Alec asks, probably hearing us through the whole in his wall.

Jonathan gives Clary a look. "Come sister, we must leave," he calls to her.

"May I have a minute to persuade him?" She asks him.

"Fine, but hurry," he commands, I glare at him, not liking the way he talks to Clary and deciding that I'm not letting her go anywhere near him ever again. I try to pull Clary into my arms as soon as he leaves the room but she pushes me away. I look into her eyes and suddenly they are the same eyes that I feel in love with. She's back!

"Jace, we don't have much time," she says in a rushed voice, her normal tone coming back as well.

"What's going on?" I ask her, the drowsiness starting to get worse.

"Jonathan thinks that I am tied to him, but I'm not. I have to act like I am so he doesn't figure out a way to make it actually work. He wants you to join his evil team for some sort of plan." Clary says hurriedly, keeping her voice barely audible.

"Jace, are you awake still?" Alec says, starting to get louder. Suddenly Jonathan flies back into the room.

"Time to go, Clarissa. We will work on him later." Jonathan snaps.

Clary nods, the glazed over version of her returning. She starts to walk toward him but I hold onto her wrist, I'm not letting her go this time. Clary gives me a hard look and the sleeping potion is starting to make me sway.

Jonathan walks over to me with a huff and with one small push I am on the ground, my eyelids weighing tons and I struggle to keep them open. I let out a cry as Jonathan takes Clary's wrist and drags her away as I can no longer move my limbs from sheer exhaustion.

"See you soon," she mouths, and with that, both her and Jonathan disappear into thin air.

**How was that? I hoped you liked it! Please give me some feedback! I'm sorry that I did another cliff-hanger! The next chapter will be longer I promise! Until then!:)**


	3. Chapter 3

**Disclaimer! I am not Cassandra Claire!**

**Thank you guys so much for all of the favorites and reviews! It makes me so happy even if the story has been pretty sad so far! **

"Why was he on the floor when you found him, I thought you said that you put him in bed?" Maryse's voice says as it floats above me.

"We did! But then Alec thought that he heard Jace talking so we went into his room and Saw Jace lying on the floor, completely out from the potion." Isabelle replies, her voice sounding distant and fuzzy just like Maryse's.

"How long after you gave him the potion did you hear him talking, Alec?" Maryse asks, her tone slowly getting sharper as I try to remember what happened. I have this nagging in the back of my mind, and the way they talk about me being passed out, makes me worry.

"About five minutes after," Alec answers, my mind starting to clear as the sinking feeling grows. Maybe I don't want to come to.

"Well then it's highly unlikely that he was actually awake talking to someone, the potion is almost impossible to fight off for more than sixty seconds," Maryse muses. "But, then again he shouldn't have been able to get out of bed either,"

I try to think back to what I last remember. My stomach plummets when I remember Clary being taken, not knowing where she is. Only there is another memory, one that confuses me. I see Clary talking like a stranger, her eyes flashing back into the ones I know so well but only for the briefest second. The suddenly there is someone else, shrouded in darkness. Jonathan.

"Look he's waking up!" Izzy exclaims, her loud voice slicing into my head with pain.

I groan and slowly sit up, feeling Alec's hands on my back helping me up as well. I shove my hair from my face and slowly blink into focus the concerned faces of Maryse, Alec, and Izzy. One thought spills out of my mouth before I can stop it. "I saw them."

"What?" Both Alec and Isabelle exclaim at the same time. Now the memory is starting to come to me clearer. I was so close. If they hadn't given me that damn potion I would have been able to kill that bastard once and for all and save Clary! I was this close!

"Clary and Jonathan. I saw them last night. I would have been able to save her had you not given me that blasted sleeping potion!" I snap, anger rushing through my head, sharpening my senses.

"Wait, they were here, as in, inside of your room last night?" Isabelle asks, a shiver running over her.

"Yes," I say harshly. "If you two hadn't gotten the grand idea to drug me, then I would have been able to fight him!"

"Or maybe the only reason they came, is because you were indisposed. Jonathan is not an idiot and would not have walked right into the heart of the institute while his only match was alert." Maryse suggests. I think this over, maybe she is right.

"What did they want?" Alec asks. "Did he just want to gloat that he had Clary while you couldn't do anything about it?"

I shake my head. "No, they wanted me to come with them. For some reason Clary has to act like she's tied to him somehow and explained that Jonathan wants me for his evil team,"

"Do you know what he plans to do?" Isabelle questions, looking worried as she fingers her long braid.

"No, they never told me. But what are we supposed to do now? Clary mouthed that she would see me soon, but when, where? Will they wait until I can't fight back again?" I spit out my thoughts like rapid fire. Now that Clary has been dangled so close before being taken away again I am in a frenzy to find her. I have let her down twice now.

"I don't know, we could possibly stage a situation," Maryse says, thinking aloud.

I lick my lips, balling my hands. "But what if he knew that I was faking?" My voice is starting to get more and more strained the longer I am awake. I am now starting to see while Alec and Izzy put me under, I sound mad. Crazier than the time I ate fairy food and we all know how that went.

"We'll get him Jace, we'll get Clary back," Alec say's as he puts an arm around me.

"What if we don't though?" I ask, sounding like a wounded puppy.

Isabelle slides her arm around my other side, her vanilla perfume filling my nose. "We will,"

**Mean while….Clary's pov**

"Why did that stupid Lightwood have to come in and check on him?" Jonathan spits. I bite my tongue to keep myself from defending Alec. Instead I focus on letting my vision narrow down until I am staring at spot on the far wall and the rest of my vision fades out.

"We will get him another time brother," I reply, trying to keep my voice monotone and lifeless, what he expects it to be. Or at least what I hoped it is supposed to sound like. After Jonathan reached out of than coffin and said we were "bonded" I was just like "The f*** you talking about?" I didn't feel any different and when he told me to do stuff I still wanted to tell him some very unlady like words, but I thought better of it. If he ever finds out that it didn't work then maybe he'll try again and do something different that would make it work, and I cannot risk that happening.

"Yes, but now he will never take more sleeping potion, or anything that could allow him to be incapacitated." Jonathan growls steeping closer to me then I would have liked. "What are we to do now?" He asks, his breath heating the side of my head as I try not to shiver with revulsion.

"I don't think we will need to wait for him to become incapacitated. I think that once we tell him what hurts you, hurts me, he will not touch you and come with us willingly." I try to persuade him without being too obvious. I need Jace to come with us fully aware.

"Hmm, that is good sister. You and I think very alike. We will set out for him as soon as he is well alone without being in reach of the others to come to the rescue," Jonathan purrs, stepping even closer to me until our bodies are almost touching. I try not to gag as I force myself to not take several steps back.

"Sounds like a plan, brother," I mutter, trying to not sound sarcastic.

"Until then,"

**Sorry it took me so long to update! I just started back at school! I hoped you liked this chapter and look forward to hearing what you think! Thank you so much for everything!:)**


	4. Chapter 4

**Disclaimer, I do not own any of the characters!**

**Sorry it took me so long to update again! This will be a short one, but I hope to update it again much faster!**

Jace POV

I sit in my bed while Alec and Isabelle are in a flurry about me. All loud voices and grand gestures but all of it just seems annoying today.

"He saw her yesterday, that means that they can't be too far away! Especially if he wants Jace for something, that means they would need to stay close!"

"But we looked everywhere within a twenty mile radius of the city, he is not in New York," Isabelle replies with finality.

"Jace, how did they leave again?" Alec asks, suddenly turning to me.

"I don't know, Clary just walked over to him, grabbed his hand, and they vanished," I manage to spit out. It kills me thinking of just how easily he was able to take her away from me again.

"He has to have something magic that we don't know about," Alec concludes unhelpfully.

"Yes, but what?" Isabelle asks. Indeed, that is the question. I need to know where to find him so I can rip his throat out and finally get Clary back in my arms.

Isabelle and Alec continue to hover over me for the rest of the day, asking me stupid questions and coming to unhelpful conclusions. I wish they would just leave already so I can sneak out can do something, anything, that could lead me to Clary. My latest plan is to burn the city to the ground so Jonathan has no where left to hide.

It is past eleven o'clock when Isabelle and Alec finally leave to go to bed. As soon as the door shuts behind them I launch myself from bed, unable to stay still for a moment longer. I throw on my hunting gear, feeling the familiar leather slide over my body.

I glance at myself in the mirror, my eyes looking hollow and sharp. Get ready Jonathan, I'm coming.

Clary's POV

"Finally, he's alone," Jonathan snaps. "We need to make our move now,"

My stomach churns with anxiety. "Whenever you're ready brother," I reply, forcing myself to place my hand in his and to not scream when as soon as it touches my body gets ripped through time and space.

**Sorry it was so short! I promise that it will be longer next time! I hoped you liked it! Please give me feedback or any ideas you want to happen in the next chapter! Thanks for reading!**


End file.
